data_3DP5 # _model_server_result.job_id TuJEXw_dgUgjuIJgXYWwPQ _model_server_result.datetime_utc '2025-04-12 16:41:41' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3dp5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":122}' # _entry.id 3DP5 # _exptl.entry_id 3DP5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3DP5 _cell.length_a 53.475 _cell.length_b 40.125 _cell.length_c 42.085 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DP5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 30 A CYS 35 1_555 C CAB HEC . A HEC 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? covale ? covale2 A SG CYS 33 A CYS 38 1_555 C CAC HEC . A HEC 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc1 A NE2 HIS 34 A HIS 39 1_555 C FE HEC . A HEC 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc2 A SD MET 74 A MET 79 1_555 C FE HEC . A HEC 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag FE NA HEC sing 129 n n FE NB HEC sing 130 n n FE NC HEC sing 131 n n FE ND HEC sing 132 n n CHA C1A HEC doub 133 n n CHA C4D HEC sing 134 n n CHA HHA HEC sing 135 n n CHB C4A HEC doub 136 n n CHB C1B HEC sing 137 n n CHB HHB HEC sing 138 n n CHC C4B HEC doub 139 n n CHC C1C HEC sing 140 n n CHC HHC HEC sing 141 n n CHD C4C HEC doub 142 n n CHD C1D HEC sing 143 n n CHD HHD HEC sing 144 n n NA C1A HEC sing 145 n y NA C4A HEC sing 146 n y C1A C2A HEC sing 147 n y C2A C3A HEC doub 148 n y C2A CAA HEC sing 149 n n C3A C4A HEC sing 150 n y C3A CMA HEC sing 151 n n CMA HMA1 HEC sing 152 n n CMA HMA2 HEC sing 153 n n CMA HMA3 HEC sing 154 n n CAA CBA HEC sing 155 n n CAA HAA1 HEC sing 156 n n CAA HAA2 HEC sing 157 n n CBA CGA HEC sing 158 n n CBA HBA1 HEC sing 159 n n CBA HBA2 HEC sing 160 n n CGA O1A HEC doub 161 n n CGA O2A HEC sing 162 n n O2A H2A HEC sing 163 n n NB C1B HEC sing 164 n y NB C4B HEC sing 165 n y C1B C2B HEC doub 166 n y C2B C3B HEC sing 167 n y C2B CMB HEC sing 168 n n C3B C4B HEC sing 169 n y C3B CAB HEC doub 170 e n CMB HMB1 HEC sing 171 n n CMB HMB2 HEC sing 172 n n CMB HMB3 HEC sing 173 n n CAB CBB HEC sing 174 n n CAB HAB HEC sing 175 n n CBB HBB1 HEC sing 176 n n CBB HBB2 HEC sing 177 n n CBB HBB3 HEC sing 178 n n NC C1C HEC sing 179 n y NC C4C HEC sing 180 n y C1C C2C HEC doub 181 n y C2C C3C HEC sing 182 n y C2C CMC HEC sing 183 n n C3C C4C HEC sing 184 n y C3C CAC HEC doub 185 e n CMC HMC1 HEC sing 186 n n CMC HMC2 HEC sing 187 n n CMC HMC3 HEC sing 188 n n CAC CBC HEC sing 189 n n CAC HAC HEC sing 190 n n CBC HBC1 HEC sing 191 n n CBC HBC2 HEC sing 192 n n CBC HBC3 HEC sing 193 n n ND C1D HEC sing 194 n y ND C4D HEC sing 195 n y C1D C2D HEC doub 196 n y C2D C3D HEC sing 197 n y C2D CMD HEC sing 198 n n C3D C4D HEC doub 199 n y C3D CAD HEC sing 200 n n CMD HMD1 HEC sing 201 n n CMD HMD2 HEC sing 202 n n CMD HMD3 HEC sing 203 n n CAD CBD HEC sing 204 n n CAD HAD1 HEC sing 205 n n CAD HAD2 HEC sing 206 n n CBD CGD HEC sing 207 n n CBD HBD1 HEC sing 208 n n CBD HBD2 HEC sing 209 n n CGD O1D HEC doub 210 n n CGD O2D HEC sing 211 n n O2D H2D HEC sing 212 n n # _atom_sites.entry_id 3DP5 _atom_sites.fract_transf_matrix[1][1] 0.0187 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024922 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.023761 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SO4 A 1 1 1 SO4 SO4 . C 3 HEC A 1 122 122 HEC HEM . D 4 HOH A 1 123 1 HOH HOH . D 4 HOH A 2 124 2 HOH HOH . D 4 HOH A 3 125 3 HOH HOH . D 4 HOH A 4 126 4 HOH HOH . D 4 HOH A 5 127 5 HOH HOH . D 4 HOH A 6 128 6 HOH HOH . D 4 HOH A 7 129 7 HOH HOH . D 4 HOH A 8 130 8 HOH HOH . D 4 HOH A 9 131 9 HOH HOH . D 4 HOH A 10 132 10 HOH HOH . D 4 HOH A 11 133 11 HOH HOH . D 4 HOH A 12 134 12 HOH HOH . D 4 HOH A 13 135 13 HOH HOH . D 4 HOH A 14 136 14 HOH HOH . D 4 HOH A 15 137 15 HOH HOH . D 4 HOH A 16 138 16 HOH HOH . D 4 HOH A 17 139 17 HOH HOH . D 4 HOH A 18 140 18 HOH HOH . D 4 HOH A 19 141 19 HOH HOH . D 4 HOH A 20 142 20 HOH HOH . D 4 HOH A 21 143 21 HOH HOH . D 4 HOH A 22 144 22 HOH HOH . D 4 HOH A 23 145 23 HOH HOH . D 4 HOH A 24 146 24 HOH HOH . D 4 HOH A 25 147 25 HOH HOH . D 4 HOH A 26 148 26 HOH HOH . D 4 HOH A 27 149 27 HOH HOH . D 4 HOH A 28 150 28 HOH HOH . D 4 HOH A 29 151 29 HOH HOH . D 4 HOH A 30 152 30 HOH HOH . D 4 HOH A 31 153 31 HOH HOH . D 4 HOH A 32 154 32 HOH HOH . D 4 HOH A 33 155 33 HOH HOH . D 4 HOH A 34 156 34 HOH HOH . D 4 HOH A 35 157 35 HOH HOH . D 4 HOH A 36 158 36 HOH HOH . D 4 HOH A 37 159 37 HOH HOH . D 4 HOH A 38 160 38 HOH HOH . D 4 HOH A 39 161 39 HOH HOH . D 4 HOH A 40 162 40 HOH HOH . D 4 HOH A 41 163 41 HOH HOH . D 4 HOH A 42 164 42 HOH HOH . D 4 HOH A 43 165 43 HOH HOH . D 4 HOH A 44 166 44 HOH HOH . D 4 HOH A 45 167 45 HOH HOH . D 4 HOH A 46 168 46 HOH HOH . D 4 HOH A 47 169 47 HOH HOH . D 4 HOH A 48 170 48 HOH HOH . D 4 HOH A 49 171 49 HOH HOH . D 4 HOH A 50 172 50 HOH HOH . D 4 HOH A 51 173 51 HOH HOH . D 4 HOH A 52 174 52 HOH HOH . D 4 HOH A 53 175 53 HOH HOH . D 4 HOH A 54 176 54 HOH HOH . D 4 HOH A 55 177 55 HOH HOH . D 4 HOH A 56 178 56 HOH HOH . D 4 HOH A 57 179 57 HOH HOH . D 4 HOH A 58 180 58 HOH HOH . D 4 HOH A 59 181 59 HOH HOH . D 4 HOH A 60 182 60 HOH HOH . D 4 HOH A 61 183 61 HOH HOH . D 4 HOH A 62 184 62 HOH HOH . D 4 HOH A 63 185 63 HOH HOH . D 4 HOH A 64 186 64 HOH HOH . D 4 HOH A 65 187 65 HOH HOH . D 4 HOH A 66 188 66 HOH HOH . D 4 HOH A 67 189 67 HOH HOH . D 4 HOH A 68 190 68 HOH HOH . D 4 HOH A 69 191 69 HOH HOH . D 4 HOH A 70 192 70 HOH HOH . D 4 HOH A 71 193 71 HOH HOH . D 4 HOH A 72 194 72 HOH HOH . D 4 HOH A 73 195 73 HOH HOH . D 4 HOH A 74 196 74 HOH HOH . D 4 HOH A 75 197 75 HOH HOH . D 4 HOH A 76 198 76 HOH HOH . D 4 HOH A 77 199 77 HOH HOH . D 4 HOH A 78 200 78 HOH HOH . D 4 HOH A 79 202 80 HOH HOH . D 4 HOH A 80 203 81 HOH HOH . D 4 HOH A 81 204 82 HOH HOH . D 4 HOH A 82 205 83 HOH HOH . D 4 HOH A 83 206 84 HOH HOH . D 4 HOH A 84 207 85 HOH HOH . D 4 HOH A 85 208 86 HOH HOH . D 4 HOH A 86 209 87 HOH HOH . D 4 HOH A 87 210 88 HOH HOH . D 4 HOH A 88 211 89 HOH HOH . D 4 HOH A 89 212 90 HOH HOH . D 4 HOH A 90 213 91 HOH HOH . D 4 HOH A 91 215 93 HOH HOH . D 4 HOH A 92 216 94 HOH HOH . D 4 HOH A 93 217 95 HOH HOH . D 4 HOH A 94 218 96 HOH HOH . D 4 HOH A 95 219 97 HOH HOH . D 4 HOH A 96 221 99 HOH HOH . D 4 HOH A 97 222 100 HOH HOH . D 4 HOH A 98 223 101 HOH HOH . D 4 HOH A 99 224 102 HOH HOH . D 4 HOH A 100 225 103 HOH HOH . D 4 HOH A 101 226 104 HOH HOH . D 4 HOH A 102 227 105 HOH HOH . D 4 HOH A 103 228 106 HOH HOH . D 4 HOH A 104 229 107 HOH HOH . D 4 HOH A 105 230 108 HOH HOH . D 4 HOH A 106 231 109 HOH HOH . D 4 HOH A 107 232 110 HOH HOH . D 4 HOH A 108 233 111 HOH HOH . D 4 HOH A 109 234 112 HOH HOH . D 4 HOH A 110 235 113 HOH HOH . D 4 HOH A 111 236 114 HOH HOH . D 4 HOH A 112 237 115 HOH HOH . D 4 HOH A 113 238 116 HOH HOH . D 4 HOH A 114 239 117 HOH HOH . D 4 HOH A 115 240 118 HOH HOH . D 4 HOH A 116 241 119 HOH HOH . D 4 HOH A 117 242 120 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 FE FE HEC . . . C 3 42.444 13.967 37.056 1 16.16 ? FE HEC 122 A 1 HETATM 2 C CHA HEC . . . C 3 44.252 14.129 39.966 1 14.27 ? CHA HEC 122 A 1 HETATM 3 C CHB HEC . . . C 3 44.124 11.098 36.197 1 15.04 ? CHB HEC 122 A 1 HETATM 4 C CHC HEC . . . C 3 40.341 13.547 34.392 1 13.29 ? CHC HEC 122 A 1 HETATM 5 C CHD HEC . . . C 3 41.173 17.082 37.592 1 15.27 ? CHD HEC 122 A 1 HETATM 6 N NA HEC . . . C 3 43.935 12.799 37.935 1 13.76 ? NA HEC 122 A 1 HETATM 7 C C1A HEC . . . C 3 44.549 13.059 39.14 1 16.25 ? C1A HEC 122 A 1 HETATM 8 C C2A HEC . . . C 3 45.574 12.021 39.351 1 15.91 ? C2A HEC 122 A 1 HETATM 9 C C3A HEC . . . C 3 45.521 11.193 38.318 1 14.3 ? C3A HEC 122 A 1 HETATM 10 C C4A HEC . . . C 3 44.478 11.657 37.406 1 13.02 ? C4A HEC 122 A 1 HETATM 11 C CMA HEC . . . C 3 46.393 9.943 38.092 1 15.55 ? CMA HEC 122 A 1 HETATM 12 C CAA HEC . . . C 3 46.6 11.945 40.514 1 18.59 ? CAA HEC 122 A 1 HETATM 13 C CBA HEC . . . C 3 46 11.77 41.868 1 21.04 ? CBA HEC 122 A 1 HETATM 14 C CGA HEC . . . C 3 47.088 12.035 42.903 1 19.72 ? CGA HEC 122 A 1 HETATM 15 O O1A HEC . . . C 3 48.325 12.193 42.593 1 20.73 ? O1A HEC 122 A 1 HETATM 16 O O2A HEC . . . C 3 46.65 12.044 44.073 1 22.1 ? O2A HEC 122 A 1 HETATM 17 N NB HEC . . . C 3 42.289 12.608 35.52 1 14.77 ? NB HEC 122 A 1 HETATM 18 C C1B HEC . . . C 3 43.076 11.482 35.384 1 13.29 ? C1B HEC 122 A 1 HETATM 19 C C2B HEC . . . C 3 42.545 10.712 34.274 1 13.68 ? C2B HEC 122 A 1 HETATM 20 C C3B HEC . . . C 3 41.491 11.393 33.765 1 12.55 ? C3B HEC 122 A 1 HETATM 21 C C4B HEC . . . C 3 41.311 12.591 34.559 1 14.57 ? C4B HEC 122 A 1 HETATM 22 C CMB HEC . . . C 3 43.219 9.389 33.81 1 14.92 ? CMB HEC 122 A 1 HETATM 23 C CAB HEC . . . C 3 40.579 10.978 32.594 1 13.82 ? CAB HEC 122 A 1 HETATM 24 C CBB HEC . . . C 3 40.008 9.71 32.607 1 16.17 ? CBB HEC 122 A 1 HETATM 25 N NC HEC . . . C 3 41.039 15.096 36.171 1 14.21 ? NC HEC 122 A 1 HETATM 26 C C1C HEC . . . C 3 40.275 14.746 35.053 1 13.69 ? C1C HEC 122 A 1 HETATM 27 C C2C HEC . . . C 3 39.383 15.849 34.755 1 13.75 ? C2C HEC 122 A 1 HETATM 28 C C3C HEC . . . C 3 39.608 16.825 35.652 1 12.33 ? C3C HEC 122 A 1 HETATM 29 C C4C HEC . . . C 3 40.647 16.369 36.535 1 14.79 ? C4C HEC 122 A 1 HETATM 30 C CMC HEC . . . C 3 38.345 15.883 33.6 1 17.43 ? CMC HEC 122 A 1 HETATM 31 C CAC HEC . . . C 3 38.95 18.248 35.737 1 13.98 ? CAC HEC 122 A 1 HETATM 32 C CBC HEC . . . C 3 37.611 18.527 35.751 1 16.47 ? CBC HEC 122 A 1 HETATM 33 N ND HEC . . . C 3 42.687 15.406 38.533 1 13 ? ND HEC 122 A 1 HETATM 34 C C1D HEC . . . C 3 41.976 16.596 38.582 1 13.73 ? C1D HEC 122 A 1 HETATM 35 C C2D HEC . . . C 3 42.188 17.222 39.886 1 11.82 ? C2D HEC 122 A 1 HETATM 36 C C3D HEC . . . C 3 43.129 16.3 40.599 1 12.27 ? C3D HEC 122 A 1 HETATM 37 C C4D HEC . . . C 3 43.392 15.198 39.703 1 14.32 ? C4D HEC 122 A 1 HETATM 38 C CMD HEC . . . C 3 41.616 18.534 40.448 1 11.46 ? CMD HEC 122 A 1 HETATM 39 C CAD HEC . . . C 3 43.701 16.48 42.032 1 15.06 ? CAD HEC 122 A 1 HETATM 40 C CBD HEC . . . C 3 42.693 15.824 42.99 1 16.47 ? CBD HEC 122 A 1 HETATM 41 C CGD HEC . . . C 3 43.262 15.893 44.377 1 18.31 ? CGD HEC 122 A 1 HETATM 42 O O1D HEC . . . C 3 43.65 14.854 44.92 1 21.91 ? O1D HEC 122 A 1 HETATM 43 O O2D HEC . . . C 3 43.344 16.971 44.972 1 16.7 ? O2D HEC 122 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #